Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	111,516	C→A	18.6%	Q196K (CAA→AAA)	USA300HOU_RS00520 →	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	111,516	0	C	A	18.6%	39.7 / 3.9	27	Q196K (CAA→AAA)	USA300HOU_RS00520	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (13/8);  new base A (2/3);  total (15/12)
Fisher's exact test for biased strand distribution p-value = 6.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.50e-01

TAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGAT  >  USA300TCH1516_ALE/111386‑111642                                                                                                                                   |                                                                                                                               tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                      <  1:67411/141‑1 (MQ=255)             cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTGAGCTCAATATCAATTAACTAAtgatga                                                                                                          >  1:136215/1‑141 (MQ=255)              aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATgatgat                                                                                                         >  2:219311/1‑141 (MQ=255)               tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTGATCTGAATATCAATTAACTAATGATGAtt                                                                                                        <  2:51592/141‑1 (MQ=255)               tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                        <  1:135624/141‑1 (MQ=255)                 aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                      <  2:134712/141‑1 (MQ=255)                      aGAAATCGAAAACTTTCAGTTTTTTGCGCAATATAGCACTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                                 >  1:70512/1‑141 (MQ=255)                        aaaaCGAAAACTTTAAGGTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                               <  1:36198/141‑1 (MQ=255)                        aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                                               <  2:105148/141‑1 (MQ=255)                         aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATGAATTAACTAATCATTATTATACTATaaa                                                                                              >  2:85148/1‑141 (MQ=18)                           tCGAAAACTTTAAGTTTTATGCGCAATATAGCAATTATAAAGATTTAATGAATTATAAAAATGGATATATATTATATAATCCAGAGGTGCCGAGTTATTCAGCTCATTATTAATTAACTAGTGATGCTTATAATGAaaaaa                                                                                            >  2:122413/1‑140 (MQ=18)                              aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGACGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                         >  2:59719/1‑141 (MQ=255)                               aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                        >  1:32162/1‑141 (MQ=255)                                         ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                              <  1:201906/141‑1 (MQ=255)                                            tttGCGCAATATAGCAATTTTAAAGATTTAATTAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCGGCTAAATATCAATTCACTAATGATGATTATAATGTAAAACAATTACGAaaaacttac                                                                           >  2:153735/1‑136 (MQ=17)                                              tGCGCAATATAGCAATTTTAACGCCTTATTCAATTATAGGGATGGCGAGGCTGCAGATAATCCAGAGGTGCCGCGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                         <  1:53836/141‑1 (MQ=17)                                                          cAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGCCATACCAACaaa                                                             >  1:71923/1‑141 (MQ=255)                                                                 aaaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCGGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACATAAAAGATATGACATACAAACAAATAAAacg                                                      >  2:186012/1‑141 (MQ=255)                                                                             aaTTAAAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                          <  1:142305/141‑1 (MQ=255)                                                                                   aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAACTGTTGTTGaaa                                    >  2:45080/1‑141 (MQ=255)                                                                                   aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAGAAAGCGCCGAAGCTGTTGTTGaaa                                    >  1:189872/1‑141 (MQ=255)                                                                                     aGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAgg                                  <  1:37740/141‑1 (MQ=255)                                                                                                tatcatatcaTCCACAGCTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                       <  1:30088/141‑1 (MQ=255)                                                                                                        aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt               <  1:219311/141‑1 (MQ=255)                                                                                                             agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGCTACAGGGAATTTAAACGGTtcata          >  2:231350/1‑140 (MQ=255)                                                                                                                  tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAACGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTg     >  2:209980/1‑141 (MQ=255)                                                                                                                     cGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGat  >  2:232864/1‑141 (MQ=255)                                                                                                                                   |                                                                                                                               TAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGAT  >  USA300TCH1516_ALE/111386‑111642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑